It looks like none of your frames reached an acceptable local minimum, so
MMPBSA.py tried taking an average of an empty list (which is clearly not
well-protected here, and results in a divide-by-zero error).
You will likely need to adjust the minimization criteria to accept a less
strict convergence tolerance or use another, better minimizer to get some
of the frames to a local minimum before running entropy calculations on
them.
HTH,
Jason
On Fri, Mar 31, 2023 at 6:30 AM Nishad Ankita Rudal via AMBER <
amber.ambermd.org> wrote:
> Dear Amber Developers,
> I am trying running nmode calculation for protein-ligand complex
> (Cytochrome system) for initial 1 or 2 frames for entropy calculation with
> the following input file and command:
>
> Input file for running GB and mode
> &general
> startframe=20, endframe=1000, interval=50,
> keep_files=2
> /
> &gb
> igb=2, saltcon=0.100,
> /
> &nmode
> maxcyc=100, nmendframe=1,
> nmode_igb=1, nmode_istrng=0.1,
> /
>
> command:
> /home/software/ambergnu/amber22/bin/MMPBSA.py -O -i mmpbsa.in -o
> FINAL_RESULTS_MMPBSA.dat -sp complex_solv_md.prmtop -cp
> complex_dry_md.prmtop -rp receptor_dry.prmtop -lp ligand.prmtop -y
> final.1.nc > progress.log
>
>
> -------------------------------------------------------------------------------------------------------------------------
>
> This calculation gives an error (pasted below) that i am unable to
> understand and find any solution for it. Please provide possible solution
> for this error or any other suggestions are also helpful.
>
> Line minimizer aborted: step at upper bound 0.0024676232
> Line minimizer aborted: step at upper bound 0.012140098
> Line minimizer aborted: step at upper bound 0.03788681
> Line minimizer aborted: step at upper bound 0.0012700911
> Line minimizer aborted: step at upper bound 0.0093337326
> Line minimizer aborted: step at upper bound 0.046959281
> Line minimizer aborted: step at upper bound 0.00019163286
> Line minimizer aborted: step at upper bound 0.079604343
> Line minimizer aborted: step at upper bound 0.00044661187
> Line minimizer aborted: step at upper bound 0.0011045502
> Line minimizer aborted: step at upper bound 0.082978387
> Line minimizer aborted: step at upper bound 0.042741479
> Line minimizer aborted: step at upper bound 0.0033774559
> Line minimizer aborted: step at upper bound 0.0049827848
> Line minimizer aborted: step at upper bound 0.0044372613
> Line minimizer aborted: step at upper bound 0.064660703
> Line minimizer aborted: step at upper bound 0.00028338204
> Line minimizer aborted: step at upper bound 0.00069139542
> Line minimizer aborted: step at upper bound 0.0016381337
> Line minimizer aborted: step at upper bound 0.00035699373
> Line minimizer aborted: step at upper bound 0.053375613
> Line minimizer aborted: step at upper bound 0.0020937967
> Line minimizer aborted: step at upper bound 0.0031216561
> Line minimizer aborted: step at upper bound 0.0037521567
> Line minimizer aborted: step at upper bound 0.00013973399
> Line minimizer aborted: step at upper bound 0.049772459
> Line minimizer aborted: step at upper bound 0.0077299037
> Line minimizer aborted: step at upper bound 0.00019173903
> Line minimizer aborted: step at upper bound 0.018564367
> Line minimizer aborted: step at upper bound 4.9858388e-05
> Line minimizer aborted: step at upper bound 0.0067258898
> Line minimizer aborted: step at upper bound 0.06992304
> Line minimizer aborted: step at upper bound 0.029330483
> Line minimizer aborted: step at upper bound 0.039871274
> Line minimizer aborted: step at upper bound 0.0046801064
> Line minimizer aborted: step at upper bound 0.0001613582
> Line minimizer aborted: step at upper bound 0.00039150803
> Line minimizer aborted: step at upper bound 0.0058031536
> Line minimizer aborted: step at upper bound 0.001378761
> Line minimizer aborted: step at upper bound 0.052916809
> Line minimizer aborted: step at upper bound 0.0015673648
> Line minimizer aborted: step at upper bound 0.0019233534
> File "/home/vadlab/Amber22/bin/MMPBSA.py", line 108, in <module>
> app.parse_output_files()
> File
> "/home/vadlab/Amber22/lib/python3.10/site-packages/MMPBSA_mods/main.py",
> line 940, in parse_output_files
> self.calc_types[key]['delta'] = BindClass(
> File
>
> "/home/vadlab/Amber22/lib/python3.10/site-packages/MMPBSA_mods/amber_outputs.py",
> line 1007, in __init__
> self.delta2()
> File
>
> "/home/vadlab/Amber22/lib/python3.10/site-packages/MMPBSA_mods/amber_outputs.py",
> line 1239, in delta2
> self.data[key] = [self.com.data[key].avg() - self.rec.data[key].avg() -
> File
>
> "/home/vadlab/Amber22/lib/python3.10/site-packages/MMPBSA_mods/amber_outputs.py",
> line 187, in avg
> return (sum(self) / len(self))
> ZeroDivisionError: division by zero
>
> Fatal Error!
> All files have been retained for your error investigation:
> You should begin by examining the output files of the first failed
> calculation.
> Consult the "Temporary Files" subsection of the MMPBSA.py chapter in the
> manual for file naming conventions.
>
> Thank you for your anticipation!
>
> Ankita Nishad
> Dept. of Med Chem
> NIPER Guwahati
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
_______________________________________________
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AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Mar 31 2023 - 06:00:02 PDT
